in run control is now an option

cpp/main.cpp

@@ -18,6 +18,7 @@
 // Classes
 #include "Vihgo.h"
 
+
 using namespace std;
 namespace po = boost::program_options;
 
@@ -157,11 +158,7 @@ int main(int argc, char* argv[])
 			return -1;
 		}
 	}
-	else
-	{
-		cerr << "No file provided as control sample BAM file : stopping" << endl;
-		return -1;
-	}
+
 
 	if( geneFile.length( ) > 0 )
 	{
@@ -178,6 +175,11 @@ int main(int argc, char* argv[])
 	}
 
 
+	if( vm.count( "stop") )
+	{
+    countStop = true;
+  }
+
 	Vihgo * App = new Vihgo( bamFile , geneFile , rtFile , integraseFile , proteaseFile, referenceFile,outputFile, codonResultFile, csFile, inRunControlBam,depthThreshold, nbThread,loggingLevel, ratioThreshold ,pvalueThreshold, countStop );
   App->mainLoop();